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Dockerfile

@@ -0,0 +1,57 @@
+# Based on Jeremiah H. Savage <[email protected]> 's kent image
+FROM fedora:28
+
+MAINTAINER Alex Kotlar <[email protected]>
+
+ENV PATH="/root/mpd-perl/bin:${PATH}" \
+    PERL5LIB="/root/perl5/lib/perl5:/root/mpd-perl/lib:${PERL5LIB}"
+
+WORKDIR /root
+
+RUN dnf install -y \
+    gcc \
+    gcc-c++ \
+    libpng-devel \
+    libuuid-devel \
+    make \
+    mariadb-devel \
+    patch \
+    perl \
+    rsync \
+    unzip \
+    wget \
+    which \
+    git \
+    openssh-clients
+
+RUN wget http://hgdownload.cse.ucsc.edu/admin/jksrc.v371.zip \
+    && unzip -q jksrc.v371.zip \
+    && rm jksrc.v371.zip
+
+RUN mkdir -p bin/x86_64 \
+    && export MACHTYPE=x86_64 \
+    && cd kent/src/ && make libs \
+    && cd lib/ && make \
+    && cd ../jkOwnLib/ && make \
+    && cd ../isPcr/ && make \
+    && cd /root && rm -rf kent
+
+WORKDIR /root
+
+RUN git clone https://bitbucket.org/wingolab/mpd-dat \
+    && mkdir /root/2bit && cd $_ \ 
+    && wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit \
+    && cd /root
+
+WORKDIR /root
+
+ADD ./ /root/mpd-perl/
+
+RUN curl -L https://cpanmin.us | perl - App::cpanminus \
+    && mkdir -p /root/perl5/lib/perl \
+    && cpanm --local-lib=/root/perl5 local::lib && eval $(perl -I /root/perl5/lib/perl5 -Mlocal::lib) \
+    && cd /root/mpd-perl && cpanm MPD.tar.gz && cpanm --installdeps . \
+    && git clone https://github.com/wingolab-org/mpd-c /root/mpd-c \
+    && cd /root/mpd-c && make
+
+WORKDIR /root/mpd-perl/

README.md

@@ -2,7 +2,29 @@
 
 This package assists in the automation of multiplex primer design. To get the most out of this package you will need the companion C code, which you can find [here (mpd-c)](http://github.com/wingolab-org/mpd-c).
 
-## Installation
+## Install in Docker
+
+Run mpd-perl inside of a Docker instance. Configured for hg38.
+
+```sh
+git clone https://github.com/wingolab-org/mpd-perl && cd $_
+docker build -t mpd ./
+
+# Run
+docker run <docker_args> mpd design.pl <mpd_args>
+```
+
+Example running MPD from within Docker:
+
+```sh
+# Assuming you have a /mnt/data and wish to mount it as /data inside of the docker container
+# that you have ~/data/markers.txt.bed with your targets, and that you wish to write to ~/data/outdir/outfile.txt
+# config/hg38.yml comes installed with this docker image, inside of the image
+# if you wish, you can pass in your own config
+docker run -v ~/data:/data mpd design.pl -b /data/markers.txt.bed -c config/hg38.yml -d ~/data/outdir -o outfile.txt
+```
+
+## Manual Installation
 
 - Compiling the c binaries. Follow the instructions here: [mpd-c](http://github.com/wingolab-org/mpd-c).
 - Clone the perl MPD package (e.g., `git clone https://github.com/wingolab-org/mpd-perl.git`).
@@ -14,6 +36,7 @@ This package assists in the automation of multiplex primer design. To get the mo
 - See examples scripts in the `ex` directory or look at the tests, specifically, `t/05-Mpd.t` to see how to build and use the MPD object.
 
 ## Optional features
+
 - The MPD package can be made to use the standalone binary for isPcr by Jim Kent. If you are not familiar with isPcr [here is a web version](https://genome.ucsc.edu/cgi-bin/hgPcr) which has details about obtaining the source code to build the stand alone binary.
 - If you use the isPcr you will need the 2bit genome of the organism.